How do I prevent VSE strips using Image Offset from being cropped before the transform effect can shrink them onto the screen?
Consider a preprocessing pass where you just create new Scaled images at the intended final size with a possible transparent border.
Suppose the Blend User had 100 images at dimension (X,Y) where for example (X = 1280, Y=800) and their final render size was .5 times (X,Y). The User might just create a [2nd new] VSE scene to quickly create a new sequence of images at the new size for final use. VSE is used to batch scale images into a new file. GIMP might do the same.  
I might even place the images in the upper right hand corner and leave a transparent border in PNG format. Suit borders to your needs.  Your already use overlays. Thus no further scaling need take place because of a transparent border.  Then many or all of the files would have the same size ... the offset would be different.
Since I cannot see your VSE strips I am not addressing them directly.  So we cant see limitations, if any, of the strip manipulations. They may be some more space efficencies possible if all that were known, yet its not a requirement.
I have not considered file names.
One could claim their is some waste of hard disk space or RAM.  Space may be cheaper than time.